assayNames	BSseq-class
assays,BSseq-method	BSseq-class
binomialGoodnessOfFit	goodnessOfFit
BS.chr22	BS.chr22
BSmooth	BSmooth
BSmooth.tstat	BSmooth.tstat
BSseq	BSseq
BSseq-class	BSseq-class
BSseqTstat	BSseqTstat-class
BSseqTstat-class	BSseqTstat-class
chisqGoodnessOfFit	goodnessOfFit
chrSelectBSseq	BSseq-class
collapseBSseq	BSseq-class
combine,BSseq,BSseq-method	BSseq-class
combineList	BSseq-class
data.frame2GRanges	data.frame2GRanges
dmrFinder	dmrFinder
end,hasGRanges-method	hasGRanges-class
end<-,hasGRanges-method	hasGRanges-class
findOverlaps,GenomicRanges,hasGRanges-method	hasGRanges-class
findOverlaps,hasGRanges,GenomicRanges-method	hasGRanges-class
findOverlaps,hasGRanges,hasGRanges-method	hasGRanges-class
fisherTests	fisherTests
getBSseq	BSseq-class
getCoverage	getCoverage
getMeth	getMeth
getStats	getStats
granges,hasGRanges-method	hasGRanges-class
hasBeenSmoothed	BSseq-class
hasGRanges-class	hasGRanges-class
length,BSseq-method	BSseq-class
length,hasGRanges-method	hasGRanges-class
matrixOrNULL-class	internals
orderBSseq	BSseq-class
pData,BSseq-method	BSseq-class
pData<-,BSseq,data.frame-method	BSseq-class
pData<-,BSseq,DataFrame-method	BSseq-class
plot.chisqGoodnessOfFit	goodnessOfFit
plotManyRegions	plotRegion
plotRegion	plotRegion
poissonGoodnessOfFit	goodnessOfFit
print.chisqGoodnessOfFit	goodnessOfFit
read.bismark	read.bismark
read.bsmooth	read.bsmooth
read.umtab	read.umtab
read.umtab2	read.umtab
sampleNames,BSseq-method	BSseq-class
sampleNames<-,BSseq,ANY-method	BSseq-class
seqlengths,hasGRanges-method	hasGRanges-class
seqlengths<-,hasGRanges-method	hasGRanges-class
seqlevels,hasGRanges-method	hasGRanges-class
seqlevels<-,hasGRanges-method	hasGRanges-class
seqnames,hasGRanges-method	hasGRanges-class
seqnames<-,hasGRanges-method	hasGRanges-class
show,BSseq-method	BSseq-class
show,BSseqTstat-method	BSseqTstat-class
start,hasGRanges-method	hasGRanges-class
start<-,hasGRanges-method	hasGRanges-class
strand,hasGRanges-method	hasGRanges-class
strand<-,hasGRanges-method	hasGRanges-class
subsetByOverlaps,GenomicRanges,hasGRanges-method	hasGRanges-class
subsetByOverlaps,hasGRanges,GenomicRanges-method	hasGRanges-class
subsetByOverlaps,hasGRanges,hasGRanges-method	hasGRanges-class
updateObject,BSseq-method	BSseq-class
width,hasGRanges-method	hasGRanges-class
width<-,hasGRanges-method	hasGRanges-class
[,BSseq-method	BSseq-class
[,BSseqTstat,ANY-method	BSseqTstat-class
[,BSseqTstat-method	BSseqTstat-class
[,hasGRanges,ANY-method	hasGRanges-class
[,hasGRanges-method	hasGRanges-class
